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W-formate dehydrogenase M405A from Desulfovibrio vulgaris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 30% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.31 46.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.874 α = 90 b = 123.833 β = 90 c = 149.891 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M 2022-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.117 75.058 92.3 0.994 8.31 6.9 47566
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.117 2.298 0.613
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6SDR 2.117 75.058 47565 2417 68.356 0.2 0.197 0.204 0.2518 0.2532 38.585
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.448 0.016 0.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.371 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 15.223 r_dihedral_angle_1_deg 7.583 r_lrange_it 6.417 r_lrange_other 6.409 r_scangle_it 4.47 r_scangle_other 4.47 r_mcangle_it 4.239 r_mcangle_other 4.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.371 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 15.223 r_dihedral_angle_1_deg 7.583 r_lrange_it 6.417 r_lrange_other 6.409 r_scangle_it 4.47 r_scangle_other 4.47 r_mcangle_it 4.239 r_mcangle_other 4.239 r_scbond_it 2.903 r_scbond_other 2.902 r_mcbond_it 2.817 r_mcbond_other 2.817 r_angle_refined_deg 1.547 r_angle_other_deg 1.216 r_symmetry_xyhbond_nbd_refined 0.87 r_nbd_other 0.231 r_nbd_refined 0.203 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.151 r_symmetry_xyhbond_nbd_other 0.094 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9149 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 185
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing XDS data reduction Aimless data scaling XSCALE data scaling pointless data scaling